Dear Christoph,
It is my misunderstanding during finding ways to solve the domain
decomposition error on Stampede. Gromacs suggests optimizing the DD grids
and choosing the proper ranks. When standalone mode is ok, I thought that
log file might give me some clue about that. Therefore, I looked at the log
file saying that csg_stat --nt 8 ...
I guessed that this may be a way to solve the error. That is why I asked it.
However, I found the answer after I tried few numbers for "mdrun -nt
option".
<mdrun>
<opts>-nt number</opts>
<mdrun>
Gromacs manual: "With thread-MPI there are additional options -nt, which
sets the total number of threads."
The IBI is running now.
Thank you for your kind answers.
Best regards,
Changwoon Jang
On Mon, Jul 25, 2016 at 4:09 PM, Christoph Junghans <[email protected]>
wrote:
> Can you explain, what the issue with csg_stat was please? Is there an
> error?
>
> 2016-07-25 12:25 GMT-06:00 Chang Woon Jang <[email protected]>:
> > Dear Christoph,
> >
> > Thank you for your reply. Does it mean that I need to set up the
> > following like
> >
> > <simulation>
> > <tasks>--nt number</tasks>
> > </simulation>
> >
> > in the <gromacs> in xml file?
> Ok, "cg.inverse.simulation.tasks" means
> <cg>
> <inverse>
> <simulation>
> <tasks>8</tasks>
> </simulation>
> </inverse>
> </cg>
> but make sure to put it in existing blocks!
>
> Christoph
>
> >
> > Thank you.
> >
> > Best regards,
> > Changwoon Jang
> >
> >
> >
> >
> >
> > On Mon, Jul 25, 2016 at 1:42 PM, Christoph Junghans <[email protected]>
> > wrote:
> >>
> >> 2016-07-25 9:59 GMT-06:00 Chang Woon Jang <[email protected]>:
> >> > Dear Votca Users,
> >> >
> >> > I would like to solve the gromacs domain decomposition error on
> >> > parallel
> >> > machine. I have asked Gromacs Users about the error. The final
> >> > conclusion is
> >> > to choose the proper number of ranks. The option "-nt 27" needs to be
> >> > included in setting file. I have tried the following options.
> >> >
> >> > <mdrun>
> >> > <opts>-nt 27</opts>
> >> > </mdrun>
> >> >
> >> > However, it does not influence the domain decomposition.
> >> >
> >> >
> >> >
> >> > I have tested standalone mode in my local machine. It works well. I
> have
> >> > looked at inverse.log file. It says "Running critical command
> 'csg_stat
> >> > --nt
> >> > 8 --options /home/tmp/settings.xml --top topol.tpr --trj traj.xtc
> >> > --begin 10
> >> > --first-frame 0'. I think this is the key issue.
> >> What is exactly is the issue with csg_stat and 8 threads?
> >> csg_stat should work with all number of threads, otherwise please
> >> report an issue:
> >> <https://github.com/votca/csg/issues>
> >>
> >> >
> >> > Therefore, how can I change csg_stat --nt "numbers" via setting.xml
> >> > file?
> >> You can limit the number of threads using the xml option
> >> "cg.inverse.simulation.tasks"!
> >>
> >> Christoph
> >> >
> >> > Thank you.
> >> >
> >> >
> >> > Best regards,
> >> > Changwoon Jang,
> >> >
> >> > Postdoctoral Research Fellow
> >> > Department of Chemical & Biological Engineering, Drexel University
> >> > 3141 Chestnut Street, Philadelphia, PA 19104
> >> >
> >> > Voice: (662) 617-2267
> >> > E-mail: [email protected]
> >> >
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> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >>
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> Christoph Junghans
> Web: http://www.compphys.de
>
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